1000 sample comparison of MLPA and RT-PCR for carrier detection and diagnostic testing for Spinal Muscular Atrophy Type 1

Charles M. Strom, Ben Anderson, Mei Peng, Urjit Patel, Corey D. Braastad, Weimin Sun

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1Quest Diagnostics Nichols Institute, San Juan Capistrano, USA 2Athena Diagnostics, Worcester, USA.

DOI: 10.4236/ojgen.2013.32014                

Abstract

Purpose: To compare the accuracy of a commercially available MLPA kit with a laboratory developed RT-PCR assay for the detection of SMN1 and SMN2 copy numbers in clinical samples. Methods: We developed and validated a laboratory developed real time PCR based test capable of detecting SMN1 and SMN2 copy numbers in individuals. We also validated an MLPA kit purchased from MRC Holland for the same purpose. We then analyzed a series of 1027 anonymized samples using both technologies. When discrepant results were obtained, each sample was re-analyzed at least twice using both platforms. Results: Five samples did not yield results in either assay. For SMN1 copy number analysis, 2 RT-PCR assays revealed indeterminant results and all 1020 other samples were concordant for SMN1 copy number. There were 9 discrepancies in SMN2 copy number determination mostly due to a variability in MLPA analysis. Conclusion: Both MLPA and RTPCR assays give a reliable estimate of SMN1 copy number and are therefore appropriate for population based carrier screening for Spinal Muscular Atrophy Type 1. The MLPA kit has a low incidence (<1%) of underestimating the SMN2 copy number by 1 copy, but this inconsistency is of little clinical significance and can be overcome by replicate testing.

Keywords

Spinal Muscular Atrophy; Carrier Screening; SMN1; SMN2; MLPA

Conflicts of Interest

The authors declare no conflicts of interest.

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